I'm not sure how the OEMs do it, but from an automotive machinist/rebuilder point of view, you square the deck, drill/ream/hone the guides, cut/grind/lap the valve seats, and machine the spring seats.
The OEM has to deal with squaring, drilling, and tapping the acessory mounting bosses, along...
I've been bored lately, and decided to design/build an engine from the ground up. I've got over a decade of experience building racecars and rebuilding engines. I've also got 5 years of experience as a machinist and access to the tools required to build it.
Where can I find books or references...